Steffen Neumann

Alignment with the mzQC folks might be nice. https://github.com/HUPO-PSI/mzQC What about a rather generic `peakQuality` function, and parameters that specify what is calculated, i.e. beta, egauss, ... Yours, Steffen

Hi, indeed that's not an xcms issue. Please check out e.g. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4796354/ which has an overview, including "strategies based on the study samples". Yours, Steffen

Hi, can't confirm on my setup, and I wouldn't recall any changes in xcms that could've caused this. ``` > library(xcms) ... > xs sessionInfo() R version 4.3.1 (2023-06-16) Platform:...

Hi, thanks for the report, we should turn this into a unit test once we've figured exactly what's going on. Yours, Steffeb

How much of that could be handled by mzTab-M ? The SMF Feature table nicely corresponds to the (grouped) xcms list. Ungrouped data is technically also kinda possible and requires...

Hi, the official docs are in https://hupo-psi.github.io/mzTab/2_0-metabolomics-release/mzTab_format_specification_2_0-M_release.html and @nilshoffmann wrote an R package to read/write mzTab-M at https://github.com/lifs-tools/rmzTab-m/ I need to find some snippets I have to export the old...

+1 for not having all that as dependency. Still, there could be an XcmsExperiment-BackendMzTabM in the mid-term, and in the short-term we have some code snippets that demonstrate import /...

+1 for not adding these dependencies. That's why I suggested a kind of XcmsExprtiment-BackendMzTabM in the mid-term. rmzTab-M was initially generated through code generation from an OpenAPI specification. Maybe someone...

Or, leave netCDF behind and go straight to export/conversion to mzML ? Can Proteowizard https://proteowizard.sourceforge.io/ convert your data ? Also, try to avoid the ancient xcms classes xcmsRaw and xcmsSet....

Could you give more information about that instrument and data ? In the netCDF I see `"QDa Positive(+) Scan (100.00-600.00)Da, Centroid, CV=15"` and `"No Chromatography" ; "Direct Inlet Probe" ;...